4  Prevalence of visible lesions seperately by SICTT and IFN-γ positive animals at slaughter

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4.1 Introduction

This document presents the prevalence of visible lesions at slaughter within bTB positive animals separately by those classified by the SICTT and IFN-γ. There was no facility within AHCS prior to May 2019 to record IFN-γ positive animals. Before this, if an animal had a positive IFN-γ result, their SICTT results were reinterpreted as positive. As a result, we have had to use old raw IFN-γ data to try and differentiate between which animals were positive on IFN-γ or SICTT. The old data has some missing tag numbers etc. and so we cannot be certain that we have assigned all cases to either IFN-γ or SICTT correctly. However, we believe, the vast majority of the data is correct. Note, currently, we seem to be missing some lesions for Dec 2023. (awaiting new data dump)

This is the difference between overall lesion prevalence document and this one (i.e. we make an attempt to seperate SICTT and IFN-γ positive trends).

4.2 Definitions

4.2.1 Proportion of animals with lesions at routine slaughter

If an animal is classified as bTB positive before entering an abattoir or a meatplant, it must have a permit to enter. Any animal with a permit will get a visual inspection for lesions. In rare instances, a bTB positive animal may be sent to a knackery instead of an abattoir or meatplant (e.g. if the animal dies before being sent to the factory). In these cases, a permit may not be issued and a visual inspection does not routinely take place in a knackery. For these reasons, only animals with a permit (and thus, a visual check completed) are considered for this document.

Of all SICTT and IFN-γ positive animals, this is the breakdown of the number of animals with a permit:

 per_type      n      percent valid_percent
     ER26 275450 0.8541270663  0.8766737004
    ER26A   2083 0.0064590549  0.0066295564
    ER26B    245 0.0007597064  0.0007797606
    ER26D    193 0.0005984626  0.0006142604
  ER26GIF  25837 0.0801164676  0.0822313247
    ER26R    281 0.0008713367  0.0008943377
    ER26S   9513 0.0294983147  0.0302769901
 ER26SGIF    597 0.0018512030  0.0019000697
     <NA>   8294 0.0257183877            NA

Of importance here is that ER26GIF and ER26SGIF permits refer to IFN-γ bTB positive animals. As mentioned above, these did not exist on AHCS prior to May 2019.

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4.3 Overall lesion prevalence (seperately by SICTT or IFN-γ)

4.3.1 All animals combined:

Figure 4.1: Overall lesion prevalence within SICTT and IFN-γ positive animals at slaughter.

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4.3.2 All animals combined monthly:

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4.3.2.1 Interactive

Figure 4.2: Overall lesion prevalence within SICTT and IFN-γ positive animals at slaughter.

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4.3.3 AHCS herd-type per year

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Figure 4.3: Overall lesion prevalence within SICTT and IFN-γ positive animals at slaughter by year.

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4.3.4 AHCS herd-type per month

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4.3.4.1 Interactive

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Figure 4.4: Overall lesion prevalence within SICTT and IFN-γ positive animals at slaughter by month and AHCS herd-type.

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4.3.5 Brock et al. herd-types per year

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Figure 4.5: Overall lesion prevalence within SICTT and IFN-γ positive animals at slaughter by Brock et al. herd-types per year.

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4.3.6 Brock et al. herd-types per month

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4.3.6.1 Interactive

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Figure 4.6: Overall lesion prevalence within SICTT and IFN-γ positive animals at slaughter by Brock et al. herd-types per month.

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4.4 Lesion prevalence by location

The following section estimates the prevalence of SICTT or IFN-γ positive animals that have lesions at different locations in the body.

4.4.1 All animals combined:

Yearly:

Figure 4.7: Overall lesion prevalence within SICTT and IFN-γ positive animals at slaughter by lesion location per year.

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Monthly version:

Figure 4.8: Overall lesion prevalence within SICTT and IFN-γ positive animals at slaughter by lesion location per month.

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4.4.2 Proportion breakdown by where the lesions are found:

(of animals with lesions, what is the proportion breakdown of where they are located)

SICTT:

Figure 4.9: Proportion of lesions by location for SICTT postive animals by year

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IFN-γ:

Figure 4.10: Proportion of lesions by location for IFN-γ postive animals by year

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4.4.3 AHCS herd-types per year

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Figure 4.11: Overall lesion prevalence within SICTT and IFN-γ positive animals at slaughter by lesion location and AHCS herd-types per year.

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4.4.4 AHCS herd-types per month

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4.4.4.1 Interactive

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Figure 4.12: Overall lesion prevalence within SICTT and IFN-γ positive animals at slaughter by lesion location and AHCS herd-types per month.

Same plot but zoomed in for clarity (outliers due to small numbers):

Figure 4.13: Overall lesion prevalence within SICTT and IFN-γ positive animals at slaughter by lesion location and AHCS herd-types per month.

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4.4.5 Brock et al. herd-types per year

Figure 4.14: Overall lesion prevalence within SICTT and IFN-γ positive animals at slaughter by lesion location and Brock et al. herd-types per year.

4.4.6 Brock et al. herd-types per month

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4.4.6.1 Interactive

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Figure 4.15: Overall lesion prevalence within SICTT and IFN-γ positive animals at slaughter by lesion location and Brock et al. herd-types per month.

Same plot but zoomed in for clarity (outliers due to small numbers):

Figure 4.16: Overall lesion prevalence within SICTT and IFN-γ positive animals at slaughter by lesion location and Brock et al. herd-types per month.

4.5 Additional things to add

  • Tables
  • Smooth trend plots

4.6 Questions

  • Why is there a peak in lesions in bTB positive animals at the start of the year (seems more pronounced in SICTT?)? Is this simply an administrative issue whereby there is a delay in sending animals to a factory?

  • Would it have anything to do with a slight increase in avian readings around Sept (this is seen in IFN-γ, we presume the same in SICTT)? The animals have been exposed to the environment for longer at this stage?

  • Avian is lower at the start of the year - is this because the majority of animals will be immunosurpressed (pregnant)(IFN-γ is mainly testing dairy animals)